The most annoying things about pets as SMN is that they don't register pet actions in a timely fashion. This is because they are animation- or GCD-locked from using their basic attack.

For example, Garuda spams Wind Blade while on Obey. So, what happens when you try to...

- Use Contagion? Well, better spam it like crazy because Garuda is probably busy. Nevermind you need it to activate very quickly in order to get the full effect (as you likely have all 4 of your DoTs up, and the longer you wait the more likely Miasma II is to fall off before Contagion goes off).
- Use Shockwave? Well, I hope you don't actually want Garuda to push anything back, because she'll probably ignore you in favor of doing Wind Blade, and even if she does recognize the command, she has to fly over to the mob first and THEN use Shockwave. Yeah... good luck with that. That's like giving WHM a Fluid Aura that takes 6 seconds to cast. Not very useful.
- Use Enkindle? Same problems as above. Which is really annoying because SMN is the only job that has to try to squeeze in so many off GCD abilities and can only do so after specific instant cast spells. As a melee, you can use an off GCD ability after ANY weapon skill. Whereas as SMN, you have to do it after Bio, Miasma II, Ruin II, or a Swiftcasted Shadow Flare. For your opener, you have to input probably twice as many actions as any other job in the same amount of time, and probably half of those abilities may not even go off because your pet is too busy ignoring you.

SO WHAT IS THE SOLUTION!?

Super easy: Make pets basic action an auto-attack, that is freely interruptable, just like player attacks. Garuda busy doing Wind Blade? WHO CARES! Just stop Wind Blade and go straight into Contagion. No need to have Wind Blade as a GCD action. Just make it an auto-attack and all the complaints about Contagion, Shockwave, Enkindle, etc. just go away! Just like magic disappear!